Python提取fasta文件成单行文件

R语言对fasta这种超大的字符文件进行处理真的是太慢了，Python是真的香啊！

import os
import time

start = time.time()

os.chdir('C:/Users/Administrator/Desktop/')
print(os.getcwd())

res_dict = {}

with open('ylg.protein.pep','r') as pep:
    for line in pep:
        if line.startswith('>'):
            name = line.strip().split()[0]
            res_dict[name] = ''
        else:
            res_dict[name] += line.replace('\n','')

print(len(res_dict))

for cds_id, sequence in res_dict.items():
    #print(cds_id)
    #print(sequence)
    #time.sleep(2)
    with open('pep.seq.txt', 'a') as file:
        file.write(cds_id.replace('>','') + "\t" + sequence + "\n")

end = time.time()
print(end - start)

4万多个基于32万多行，耗时5.12s。和R相比真的是很快了。

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